The correct question is "where are the scissors?" - this normally refers to one pair of scissors but depending on the context it can be used to refer to multiple pairs of scissors. Scissors shoes and glasses are all plural nouns because they all refer to a pair of something (pair of scissors, pair of shoes, pair of glasses) if glasses were to be broken in half they would no longer function as glasses therefore they must always function as a pair - one glass for the left eye, one glass for the right. The same goes for scissors; shoes on the other hand can be separated so you would use "where is the shoe?" (Singular) "where are the shoes" (plural) whereas if we were talking about pants it would be - "where are the pants?" (Singular) "where are the pants?" (Plural) because pants can't be separated into two functioning parts.

Number two is correct: where are the scissors? Also, we always ask "where are my glasses?", and if we lost both shoes, we'll say "where are my shoes?". Of course, if you've lost a single show, you can say "where is my shoe?"